In certain methods, a plurality of oligonucleotide tags are attached to polynucleotides of initial nucleic acid sample to provide a tagged sample in which substantially every target polynucleotide molecule in the sample is attached to a different oligonucleotide tag, i.e., a oligonucleotide tag that has a sequence that is different to other oligonucleotide tags. After the target polynucleotides have been amplified, the number of target polynucleotides in the initial nucleic acid sample can be estimated by counting the number of different tags that are associated with the amplified target polynucleotides. The plurality of tags can be thought of as a counter sequence because they provide a way that individual polynucleotide molecules can be counted, even after they are amplified.